Interacting with the biomolecular solvent accessible surface via a haptic feedback device

Background  

From the 1950s computer based renderings of molecules have been produced to aid researchers in their understanding of biomolecular structure and function. A major consideration for any molecular graphics software is the ability to visualise the three dimensional structure of the molecule. Traditionally, this was accomplished via stereoscopic pairs of images and later realised with three dimensional display technologies. Using a haptic feedback device in combination with molecular graphics has the potential to enhance three dimensional visualisation. Although haptic feedback devices have been used to feel the interaction forces during molecular docking they have not been used explicitly as an aid to visualisation.     

Computer simulated modeling of biomolecular systems.

This paper describes the algorithm of a program used to simulate three dimensional models of molecules. In addition to open ended molecules the program also enables simulation of structures with constraints in the form of cyclic regions or fixed location of particular atoms. Several molecules can be handled in a single run and each molecule can have any number of contraints. Further, any number of conformations can be obtained for each constrained region. The program can be used for research in several areas of molecular biology, e.g., structure determination, conformational analysis and topographic comparisons.     

Three‐dimensional digitization of the arid land plant Haloxylon ammodendron using a consumer‐grade camera

Plant structural parameters are important for ecological studies and for monitoring the environment. Terrestrial laser scanning has become a widely accepted technique for acquiring accurate high‐density three‐dimensional information about plant surfaces; however, this instrument is expensive, technically challenging to operate, heavy, and difficult to transport to hard‐to‐reach areas such as dense forests and undeveloped areas without easy vehicle access. Using Haloxylon ammodendron, a plant widely distributed in arid lands, as an example, we used a consumer‐grade handheld camera to take a series of overlapping images of this plant. Computer vision and photogrammetric software were used to reconstruct highly detailed three‐dimensional data of the plant surface. This surface data was compared to the point cloud of the plant acquired from concomitant terrestrial laser scanning. We demonstrated that the accuracy and degree of completeness of the image‐derived point clouds are comparable to that of laser scanning. Plant structural parameters (such as tree height and crown width) and three‐dimensional models extracted from the point clouds also agree well with a relative difference of less than 5%. Our case study shows that a common camera and image processing software can be an affordable, highly portable, and viable option for acquiring accurate and detailed high‐density and high‐resolution three‐dimensional information about plant structure in the environment. This digitization technique can record the plant and its surrounding environment effectively and efficiently, and it can be applied to many ecological fields and studies.     

The protective role of a natural inhibitor in the fluorescent location of cells possessing a latent form of cell surface protease.

Leukaemia cells possess a latent form of a cell surface protease referred to as guanidinobenzoatase. Latency is due to complex formation between an inhibitor protein and the cell surface enzyme which is stable under acid conditions but is dissociated with formaldehyde treatment. The latent form of the cell surface protease has been used as a protecting mechanism during a preliminary step to stain all the nuclei of cells with haematoxylin. The enzyme-inhibitor complex was then dissociated and a combination of 9-amino acridine and propidium iodide employed to enable the fluorescent location of cells possessing active guanidinobenzoatase. We were thus able to visualise the nuclei by conventional light microscopy and simultaneously visualise the cell surface of leukaemia cells by fluorescent microscopy. This simple model system has provided technology applicable to the more complex analysis of neoplastic cells in cervical smears.     

Conformational and molecular interaction studies of glucagon-like peptide-2 with its N-terminal extracellular receptor domain

Glucagon-like peptide-2 (GLP-2) is a therapeutic target used in the treatment of short bowel syndrome. In this paper, we present the three dimensional solution structure of GLP-2 peptide determined using nuclear magnetic resonance (NMR) and molecular modelling. The GLP-2 adopts an α-helical conformation similar to that of secretin family of hormones. In order to understand the molecular details governing the ligand binding and receptor activation, macromolecular docking studies were performed between the N-terminal extracellular domain of GLP-2 receptor and the GLP-2 hormone using a data driven docking program.     

Visualisation and Quantification of Morphogen Gradient Formation in the Zebrafish

During embryonic development, signalling molecules known as morphogens act in a concentration-dependent manner to provide positional information to responding tissues. In the early zebrafish embryo, graded signalling by members of the nodal family induces the formation of mesoderm and endoderm, thereby patterning the embryo into three germ layers. Nodal signalling has also been implicated in the establishment of the dorso-ventral axis of the embryo. Although one can infer the existence of nodal gradients by comparing gene expression patterns in wild-type embryos and embryos in which nodal signalling is diminished or augmented, real understanding can only come from directly observing the gradients. One approach is to determine local ligand concentrations in the embryo, but this is technically challenging, and the presence of inhibitors might cause the effective concentration of a ligand to differ from its actual concentration. We have therefore taken two approaches to visualise a direct response to nodal signalling. In the first, we have used transgenic embryos to study the nuclear accumulation of a Smad2-Venus fusion protein, and in the second we have used bimolecular fluorescence complementation to visualise the formation of a complex between Smad2 and Smad4. This has allowed us to visualise, in living embryos, the formation of a graded distribution of nodal signalling activity. We have quantified the formation of the gradient in time and space, and our results not only confirm that nodal signalling patterns the embryo into three germ layers, but also shed light on its role in patterning the dorso-ventral axis and highlight unexpected complexities of mesodermal patterning.     

A simple method to display molecular orbitals with computer graphics

A computer program named LOBE was developed to draw molecular orbitals as lobes on a graphic display. With this program, any molecular orbital of large molecules can be displayed quickly. This program is suitable not only for general-purpose computers but also for microcomputers. A sample application is used to illustrate the program.     

SIMS: computation of a smooth invariant molecular surface.

SIMS, a new method of calculating a smooth invariant molecular dot surface, is presented. The SIMS method generates the smooth molecular surface by rolling two probe spheres. A solvent probe sphere is rolled over the molecule and produces a Richards-Connolly molecular surface (MS), which envelops the solvent-excluded volume of the molecule. In deep crevices, Connolly's method of calculating the MS has two deficiencies. First, it produces self-intersecting parts of the molecular surface, which must be removed to obtain the correct MS. Second, the correct MS is not smooth, i.e., the direction of the normal vector of the MS is not continuous, and some points of the MS are singular. We present an exact method for removing self-intersecting parts and smoothing the singular regions of the MS. The singular MS is smoothed by rolling a smoothing probe sphere over the inward side of the singular MS. The MS in the vicinity of singularities is replaced with the reentrant surface of the smoothing probe sphere. The smoothing method does not disturb the topology of a singular MS, and the smooth MS is a better approximation of the dielectric border between high dielectric solvent and the low dielectric molecular interior. The SIMS method generates a smooth molecular dot surface, which has a quasi-uniform dot distribution in two orthogonal directions on the molecular surface, which is invariant with molecular rotation and stable under changes in the molecular conformation, and which can be used in a variety of implicit methods of modeling solvent effects. The SIMS program is faster than the Connolly MS program, and in a matter of seconds generates a smooth dot MS of a 200-residue protein. The program is available from the authors on request (see http:@femto.med.unc.edu/SIMS).     

Characterisation and computational analysis of a novel lipase nanobio-based reagent for visualising latent fingerprints on water-immersed glass slides

Considering the significant evidential values of fingerprints in underwater criminal investigations and the need to visualise them using a user- and environmentally-friendly reagent, development of a novel, rapid and relatively greener nanobio-based reagent (NBR) is deemed beneficial. Lipase from the commercial Candida rugosa immobilised onto acid-functionalised multi-walled carbon nanotubes (NBR) was used as the safer and cheap lipid-sensing reagent to visualise groomed whole/split fingerprints on non-porous objects immersed in stagnant tap water for up to 30 days under a laboratory-controlled setting. Attenuated Total Reflectance – Fourier Transform Spectrometry, Field Emission Scanning Electron Microscopy and bioinformatics (molecular docking and molecular dynamics simulations) were employed to characterise and confirm the attachment of NBR onto the lipid constituents of wet fingerprints. Chromatographic results further confirmed the presence of n-hexadecanoic and octadecanoic acids on fingerprints up to 30 days of immersion. Thus, NBR may potentially be useful as the future state-of-the-art fingerprint visualisation technology.     

喇曼光谱技术在生物医学中的应用

喇曼光谱技术是一种非侵入、非弹性散射技术,能够在分子层次上探测物质的临床医学特征和结构特征。本文综述了近十年来喇曼光谱技术在生物医学中的最新发展,归纳出了四种目前在生物医学中最为活跃的喇曼光谱技术：近红外喇曼光谱、紫外共振喇曼光谱、表面增强喇曼光谱和多维喇曼成像技术。详细阐述了这四种技术的特点和适用范围,并且列举了丰富的成功范例。     

McVol - A program for calculating protein volumes and identifying cavities by a Monte Carlo algorithm

In this paper, we describe a Monte Carlo method for determining the volume of a molecule. A molecule is considered to consist of hard, overlapping spheres. The surface of the molecule is defined by rolling a probe sphere over the surface of the spheres. To determine the volume of the molecule, random points are placed in a three-dimensional box, which encloses the whole molecule. The volume of the molecule in relation to the volume of the box is estimated by calculating the ratio of the random points placed inside the molecule and the total number of random points that were placed. For computational efficiency, we use a grid-cell based neighbor list to determine whether a random point is placed inside the molecule or not. This method in combination with a graph-theoretical algorithm is used to detect internal cavities and surface clefts of molecules. Since cavities and clefts are potential water binding sites, we place water molecules in the cavities. The potential water positions can be used in molecular dynamics calculations as well as in other molecular calculations. We apply this method to several proteins and demonstrate the usefulness of the program. The described methods are all implemented in the program McVol, which is available free of charge from our website at .     

Interpretation of electron density with stereographic roadmap projections

The program RIVEM (Radial Interpretation of Viral Electron density Maps) was developed to project density radially onto a sphere that is then presented as a stereographic diagram. This permits features resulting from an asymmetric reconstruction to be projected and positioned onto an icosahedral virus surface. The features that constitute the viral surface can also be simultaneously represented in terms of atoms, amino acid residues, potential charge distribution, and surface topology. The procedure can also be adapted for the investigation of various molecular interactions.     

Inhibition of protein-protein interactions: the discovery of druglike beta-catenin inhibitors by combining virtual and biophysical screening

The interaction between beta-catenin and Tcf family members is crucial for the Wnt signal transduction pathway, which is commonly mutated in cancer. This interaction extends over a very large surface area (4800 A(2)), and inhibiting such interactions using low molecular weight inhibitors is a challenge. However, protein surfaces frequently contain "hot spots," small patches that are the main mediators of binding affinity. By making tight interactions with a hot spot, a small molecule can compete with a protein. The Tcf3/Tcf4-binding surface on beta-catenin contains a well-defined hot spot around residues K435 and R469. A 17,700 compounds subset of the Pharmacia corporate collection was docked to this hot spot with the QXP program; 22 of the best scoring compounds were put into a biophysical (NMR and ITC) screening funnel, where specific binding to beta-catenin, competition with Tcf4 and finally binding constants were determined. This process led to the discovery of three druglike, low molecular weight Tcf4-competitive compounds with the tightest binder having a K(D) of 450 nM. Our approach can be used in several situations (e.g., when selecting compounds from external collections, when no biochemical functional assay is available, or when no HTS is envisioned), and it may be generally applicable to the identification of inhibitors of protein-protein interactions.     

DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts

A program, DipoCoup, is presented that allows to search the protein data bank for proteins which have a three dimensional fold that is at least partially homologous to a protein under investigation. The three dimensional homology search uses secondary structure alignment based on chemical shifts and dipolar couplings or pseudocontact shifts for the three dimensional orientation of secondary structure elements. Moreover, the program offers additional tools for handling and analyzing dipolar couplings.     

Serological typing of meningococci by means of micro-precipitation

Summary With the aid of a microprecipitation technique on slides, it is possible to visualise, within 18 hours, precipitation lines specific for type A and C meningococci. The slides can be stored after drying and staining, and can be directly used in projection. Among a number of strains not typable with the standard sera, three new types were identified by means of agglutination and precipitation. Provisionally they were called type X, Y and Z. Strains of type X and Y were isolated from patients and carriers, those of type Z up till now only from carriers.     

Generalised Chromaticity Diagrams for Animals with <Emphasis Type="Italic">n</Emphasis>-chromatic Colour Vision

Chromaticity diagrams for tri- and tetrachromatic animals (with three and four cone classes in their retina, respectively, contributing to colour perception) are widely used in studies of animal colour vision. These diagrams not only allow the graphical representation of perceived colours, but the coordinates of colours plotted within these diagrams can be used to extract colour metrics, such as hue and chroma, or can be used directly in statistical analyses, and therefore aid our understanding of vision-mediated behaviour. However, many invertebrate species have more than four cone classes in their retina, and may therefore have pentachromatic or hexachromatic (or greater) vision. This paper describes an extension to the triangular and tetrahedral chromaticity diagrams commonly used for tri- and tetrachromats, respectively, that allows colour coordinates (and hence colour metrics) to be calculated for animals with more than four cone classes. Because the resulting chromaticity diagrams have more than three dimensions, meaningful ways to visualise the spatial position of plotted colours are discussed.     

Monitoring the wall mechanics during stent deployment in a vessel

Clinical trials have reported different restenosis rates for various stent designs. It is speculated that stent-induced strain concentrations on the arterial wall lead to tissue injury, which initiates restenosis. This hypothesis needs further investigations including better quantifications of non-uniform strain distribution on the artery following stent implantation. A non-contact surface strain measurement method for the stented artery is presented in this work. ARAMIS stereo optical surface strain measurement system uses two optical high speed cameras to capture the motion of each reference point, and resolve three dimensional strains over the deforming surface. As a mesh stent is deployed into a latex vessel with a random contrasting pattern sprayed or drawn on its outer surface, the surface strain is recorded at every instant of the deformation. The calculated strain distributions can then be used to understand the local lesion response, validate the computational models, and formulate hypotheses for further in vivo study.     

HuC–eGFP mosaic labelling of neurons in zebrafish enables in vivo live cell imaging of growth cones

The field of axon guidance is taking advantage of the powerful genetic and imaging tools that are now available to visualise growth behaviour in living cells, both in vivo and in real time. We have developed a method to visualise individual neurons within the living zebrafish embryo which provides exceptional cellular resolution of growth cones and their filopodia. We generated a DNA construct in which the HuC promoter drives expression of eGFP. Injection of the plasmid into single cell fertilised zebrafish egg resulted in mosaic expression of eGFP in neurons throughout the developing embryo. By manipulating the concentration of injected plasmid, it was possible to optimise the numbers of neurons that expressed the construct so that individual growth cones could be easily visualised. We then used time-lapse high magnification widefield epifluorescence microscopy to visualise the growth cones as they were exploring their environment. Growth cones both near the surface of the embryo as well as deep within the developing brain of embryos at 20?h post fertilisation were clearly imaged. With time-lapse sequence imaging with intervals between frames as frequent as 1?s there was minimal loss of fluorescence intensity and the dynamic nature of the growth cones became evident. This method therefore provides high magnification, high resolution time-lapse imaging of living neurons in vivo and by use of widefield epifluorescence rather than confocal it is a relatively inexpensive microscopy method.     

eF-site and PDBjViewer: database and viewer for protein functional sites

The electrostatic-surface of functional site (eF-site) is a database for the molecular surfaces of protein functional sites. To enable browsing of each molecular surface along with the atomic model, we have developed a new three-dimensional interactive viewer, PDBjViewer, that can be used both as an applet and as a stand-alone program. AVAILABILITY: The eF-site database and PDBjViewer are freely available from http://www.pdbj.org/eF-site/